RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.8nsSAE/RM_1740385.TueNov191042172024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1732041737 Database = /scratch/tmp/rModeler.8nsSAE/GCA_964204865.1_kaStyClav1.hap1.1 - Sequences = 389 - Bases = 377969001 - N50 = 24297679 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 30563765-32746820 | [ 2 ] 28380710-30563764 | [ ] 26197656-28380710 | [ ] 24014601-26197655 | [ 5 ] 21831546-24014600 | [ 4 ] 19648492-21831546 | [ 3 ] 17465437-19648491 | [ 1 ] 15282382-17465436 | [ ] 13099328-15282382 | [ ] 10916273-13099327 | [ ] 8733218-10916272 | [ ] 6550164-8733218 | [ ] 4367109-6550163 | [ ] 2184054-4367108 | [ ] 1000-2184054 |************************************************** [ 374 ] Storage Throughput = excellent ( 1264.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016471 bp ( 40016071 non ambiguous ) - Num Contigs Represented = 75 - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:08 (hh:mm:ss) Elapsed Time Round Time: 00:12:51 (hh:mm:ss) Elapsed Time : 790 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15069 repeats masked totaling 3184830 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031625 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10031625 bp After Masking: 6115094 bp Masked: 39.04 % -- Input Database Coverage: 10031625 bp out of 377969001 bp ( 2.65 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:03:15 (hh:mm:ss) Elapsed Time, 11460 HSPs Collected Number of families returned by RECON: 861 Round Time: 00:04:36 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47988 repeats masked totaling 9951637 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024846 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 30024446 bp After Masking: 18007367 bp Masked: 40.02 % -- Input Database Coverage: 40056471 bp out of 377969001 bp ( 10.60 % ) Sampling Time: 00:03:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:14:58 (hh:mm:ss) Elapsed Time, 75622 HSPs Collected Number of families returned by RECON: 3141 Round Time: 00:18:30 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149749 repeats masked totaling 29827858 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037884 bp Num Contigs Represented = 148 Non ambiguous bp: Initial: 90035884 bp After Masking: 54534775 bp Masked: 39.43 % -- Input Database Coverage: 130094355 bp out of 377969001 bp ( 34.42 % ) Sampling Time: 00:08:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2671516 Comparison Time: 01:34:10 (hh:mm:ss) Elapsed Time, 289858 HSPs Collected Number of families returned by RECON: 9783 Round Time: 01:50:04 (hh:mm:ss) Elapsed Time : 424 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 466399 repeats masked totaling 97503005 bp(s). - TE Masking time 00:08:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 247874341 bp Num Contigs Represented = 283 Non ambiguous bp: Initial: 247869941 bp After Masking: 133948564 bp Masked: 45.96 % -- Input Database Coverage: 377968696 bp out of 377969001 bp ( 100.00 % ) Sampling Time: 00:28:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 19917516 Comparison Time: 08:31:26 (hh:mm:ss) Elapsed Time, 812198 HSPs Collected Number of families returned by RECON: 28299 Round Time: 09:24:49 (hh:mm:ss) Elapsed Time : 932 families discovered. RepeatScout/RECON discovery complete: 2225 families found Classification Time: 01:22:01 (hh:mm:ss) Elapsed Time Program Time: 13:12:51 (hh:mm:ss) Elapsed Time